Variant report

Variant	rs7057286
Chromosome Location	chrX:153713787-153713788
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:30)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:30 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chrX:153711098..153721097-chrX:153740825..153747830,28	MCF-7	breast:
2	chrX:153711537..153716459-chrX:153767417..153772470,5	K562	blood:
3	chrX:153712862..153716379-chrX:153773449..153776383,5	MCF-7	breast:
4	chrX:153605453..153609525-chrX:153712051..153716179,6	MCF-7	breast:
5	chrX:153605593..153609893-chrX:153711571..153716768,6	K562	blood:
6	chrX:153671368..153673500-chrX:153711760..153714684,2	K562	blood:
7	X:153657611-153671976..X:153701576-153715648	Hela-S3	cervix:
8	chr20:52824614..52827050-chrX:153713627..153715899,2	MCF-7	breast:
9	chrX:153624545..153632466-chrX:153709449..153721332,27	K562	blood:
10	chrX:153713288..153721499-chrX:153767815..153773161,10	MCF-7	breast:
11	chrX:153697571..153703616-chrX:153709529..153715825,8	MCF-7	breast:
12	chrX:153691004..153695395-chrX:153711545..153717567,7	MCF-7	breast:
13	chrX:153624383..153633652-chrX:153704408..153721325,48	MCF-7	breast:
14	chrX:153624542..153632362-chrX:153710560..153721332,23	K562	blood:
15	chrX:153639142..153641724-chrX:153713465..153715375,4	MCF-7	breast:
16	chrX:153711592..153716888-chrX:153760694..153766504,10	MCF-7	breast:
17	chrX:153713355..153716352-chrX:153738180..153740001,2	K562	blood:
18	chrX:153674318..153677222-chrX:153712203..153714813,3	K562	blood:
19	chrX:153713383..153715797-chrX:153769453..153771661,2	K562	blood:
20	chrX:153598007..153604368-chrX:153709391..153720590,15	MCF-7	breast:
21	chrX:153711607..153725784-chrX:153738770..153748754,27	K562	blood:
22	chrX:153635755..153638655-chrX:153711241..153715335,3	K562	blood:
23	chrX:153711367..153718079-chrX:153742298..153748484,13	K562	blood:
24	chrX:153596460..153601893-chrX:153713560..153721410,16	MCF-7	breast:
25	chrX:153576705..153579564-chrX:153713461..153716046,2	MCF-7	breast:
26	chrX:153684734..153690386-chrX:153710045..153718317,11	K562	blood:
27	chrX:153661692..153667668-chrX:153711020..153716574,8	MCF-7	breast:
28	chrX:153713080..153721291-chrX:153722442..153727868,15	K562	blood:
29	chrX:153684737..153690252-chrX:153712522..153716734,15	MCF-7	breast:
30	chrX:153601928..153604764-chrX:153713001..153716367,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000071553	Chromatin interaction
ENSG00000102119	Chromatin interaction
ENSG00000207165	Chromatin interaction
ENSG00000071859	Chromatin interaction
ENSG00000101132	Chromatin interaction
ENSG00000264484	Chromatin interaction
ENSG00000264631	Chromatin interaction
ENSG00000147403	Chromatin interaction
ENSG00000073009	Chromatin interaction
ENSG00000130827	Chromatin interaction
ENSG00000071889	Chromatin interaction
ENSG00000102125	Chromatin interaction
ENSG00000196924	Chromatin interaction
ENSG00000160211	Chromatin interaction
ENSG00000013563	Chromatin interaction
ENSG00000264783	Chromatin interaction
ENSG00000261773	Chromatin interaction
ENSG00000203879	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1050047	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12392447	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.80[TSI][hapmap]
rs2071429	0.82[CEU][hapmap]
rs2315325	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap]
rs2472393	1.00[ASW][hapmap];0.82[CEU][hapmap]
rs4542114	0.86[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap]
rs4898389	0.82[CEU][hapmap]
rs5945100	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs5945195	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap]
rs5945429	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.80[TSI][hapmap]
rs5945431	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs5945433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs5945434	1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap]
rs5986979	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap]
rs5986981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs5987266	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs5987267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7051615	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7886727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33199	chrX:152864376-153820241	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	276 gene(s)	inside rSNPs	diseases
2	nsv528291	chrX:152864376-153827637	Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	277 gene(s)	inside rSNPs	diseases
3	nsv915605	chrX:153333946-153783638	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
4	nsv519042	chrX:153348431-153829693	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
5	nsv532962	chrX:153564946-153870337	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	199 gene(s)	inside rSNPs	diseases
6	nsv532963	chrX:153576890-153822717	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	195 gene(s)	inside rSNPs	diseases
7	nsv530281	chrX:153622940-153783184	Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
8	nsv532964	chrX:153622940-153854307	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7057286	LAGE3	cis	lymphoblastoid	seeQTL
rs7057286	SLC10A3	cis	lymphoblastoid	seeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:153707200-153714200	Weak transcription	Ovary	ovary
2	chrX:153707600-153714200	Weak transcription	Small Intestine	intestine
3	chrX:153707800-153714000	Weak transcription	HSMMtube	muscle
4	chrX:153708000-153713800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chrX:153708000-153713800	Weak transcription	Psoas Muscle	Psoas
6	chrX:153708000-153713800	Weak transcription	Rectal Smooth Muscle	rectum
7	chrX:153708000-153714000	Weak transcription	Brain Substantia Nigra	brain
8	chrX:153708200-153713800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chrX:153708200-153713800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chrX:153710200-153719600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
11	chrX:153711400-153713800	ZNF genes & repeats	Fetal Brain Female	brain
12	chrX:153711400-153714000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chrX:153711400-153714200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chrX:153711400-153718600	ZNF genes & repeats	Fetal Stomach	stomach
15	chrX:153711600-153714000	Transcr. at gene 5' and 3'	K562	blood
16	chrX:153711800-153713800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chrX:153711800-153713800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chrX:153711800-153713800	Genic enhancers	Right Ventricle	heart
19	chrX:153711800-153714000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
20	chrX:153711800-153714200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chrX:153711800-153714200	Enhancers	Liver	Liver
22	chrX:153712000-153713800	Genic enhancers	Primary T cells fromperipheralblood	blood
23	chrX:153712000-153714000	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chrX:153712000-153714000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chrX:153712000-153714000	Genic enhancers	Fetal Muscle Leg	muscle
26	chrX:153712400-153713800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
27	chrX:153712400-153713800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
28	chrX:153712400-153714000	Genic enhancers	Primary monocytes fromperipheralblood	blood
29	chrX:153712400-153714000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chrX:153712400-153714200	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chrX:153712400-153714400	Enhancers	Placenta Amnion	Placenta Amnion
32	chrX:153712600-153713800	Genic enhancers	Brain Inferior Temporal Lobe	brain
33	chrX:153712600-153713800	Enhancers	Colonic Mucosa	Colon
34	chrX:153712600-153713800	Genic enhancers	Gastric	stomach
35	chrX:153712600-153714000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chrX:153712600-153714000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chrX:153712600-153714000	Genic enhancers	Adipose Nuclei	Adipose
38	chrX:153712600-153714000	Genic enhancers	Fetal Intestine Large	intestine
39	chrX:153712600-153714000	Genic enhancers	Fetal Intestine Small	intestine
40	chrX:153712600-153714000	Genic enhancers	Fetal Muscle Trunk	muscle
41	chrX:153712600-153714000	Enhancers	Left Ventricle	heart
42	chrX:153712600-153714000	Enhancers	Stomach Mucosa	stomach
43	chrX:153712600-153714200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
44	chrX:153712600-153714200	Genic enhancers	Spleen	Spleen
45	chrX:153712600-153714400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
46	chrX:153712600-153714400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
47	chrX:153712600-153714600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
48	chrX:153712800-153713800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chrX:153712800-153713800	Genic enhancers	Brain Angular Gyrus	brain
50	chrX:153712800-153713800	Strong transcription	Fetal Lung	lung

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